The purpose of this project is to develop methodology for analyzing molecular population genetic data. Work has focused on statistical methods for localizing susceptibility loci for complex diseases and quantitative traits in humans. For late onset diseases, nonstandard family-based tests of association are required because parental data are often missing. We have shown that a commonly used test has a bias when there are multiple affected sibs. This bias inflates the type 1 error and can cause problems when interpreting the test results. We have developed a new test that does not have the bias. We have generalized previous single SNP results on genotyping error and power calculations to short haplotypes. These results are important because of the emerging haplotype database.